The brain will entrain to the strongest stimulus. If you combine binaural beats with isochronic tones, your brainwaves will entrain to the isochronic tones. If anything, when you combine the two I believe it makes the track less effective because it makes it harder for the brain to decipher between the two and synchronise to a single beat. There are lots of websites with compelling marketing about the benefits of combining the two together in some funky way, but I haven’t seen any research or lots of anecdotal feedback even to suggest it’s effective to combine them.

Brainwave entrainment is a method which utilizes frequencies of the brain in order to bring about specific desired thoughts and behavior. In other words, brainwave entrainment is used to induce different brainwave states related to: enhanced focus, relaxation, sleep induction, meditation, etc. With the help of a specific stimulus, aural (audio), photic (visual) or the combination of the two, we naturally induce the brain to respond by synchronizing with the stimulus frequency; this is called the “frequency following response”. The assumption is that the human brain has a tendency to change its dominant Electroencephalography frequency (recording of electrical activity along the scalp) towards the frequency of a dominant external stimulus. This is why we also talk about “brainwave synchronization”.
Another consideration of stress is whether it is acute or chronic. “Acute stress” is what an individual experiences at the time the stressor is encountered (4). The stress response is activated, and the body returns to homeostasis once the challenge of the stressor is removed or the person successfully manages the situation. For example, an individual on the way to an important meeting gets into a traffic jam and realizes she is going to be late; the stress response starts. When she calls her boss and learns that she can conference into the meeting while on the road, the stress response subsides with the resolution of the situation. When an individual experiences acute stress on a consistent basis, such as with overcommitting at work or constant worrying, it is referred to as “acute episodic stress” (4). Individuals who experience acute episodic stress often show signs and symptoms of stress (Table 1) that can negatively impact physical and psychological health. These individuals can learn how to change behaviors and manage their stress to prevent these consequences.
“One of the best ways to explain how brainwave entrainment works is by observing the effect of a tuning fork on a guitar string,” says Naik. “Hit a tuning fork tuned to a particular sound frequency, such as the note C, and hold it close to the strings of a guitar. You will notice that the C string on the guitar starts to vibrate because it has entrained on to the same frequency of the tuning fork.”
A simple spinal twist can help you get a better night's sleep. It alleviates tension that's built up in your lower back throughout the day. Sitting on your bed with legs crossed, place your right hand down on the bed behind you and rest your left hand on your right knee. Sit up straight and inhale for four to eight counts, lengthening your spine as you breathe. On your exhale, begin to twist toward your right hand (don't strain your neck). Hold this position for four more full breaths, lengthening your spine on the inhales and deepening your twist on the exhales, if it feels comfortable. Repeat yoga asanas on opposite side. (These stress-reducing yoga poses also help calm anxiety.)
Experts haven't figured out why having your body pressed and prodded works wonders, but they know that it does. Studies suggest massage can speed up weight gain in premature babies, improve lung function in asthmatics and boost immunity in men with HIV. If you can't indulge in regular full-body massages, treat yourself to the occasional pedicure, manicure or facial—all nurturing, hands-on treats that offer some of the mind-body benefits of massage. 

When your mind is all over the place, organizing your thoughts into a quick to-do list can help transfer the burden from your brain to paper. But for some people, seeing a long list of tasks can increase stress. Miller has another idea: a “stressor and action” sheet. “Fold a piece of paper in half length wise, and on the left column write ‘stressor’ and on the right hand column write ‘action,’” she says. “You will find as you write down thoughtful action steps to the things that are stressing you out, you regain authority over circumstance.” These are the signs you’re more stressed than you realize.

The thing about conditioning is, it doesn’t matter whether the conditioned response is pleasant or unpleasant, desirable or undesirable. The process of conditioning works just as well both ways. You went looking for any indication you were getting an effect by using entrainment and you happened to have an unpleasant experience that you focused on. To the mind it is irrelevant whether it was pleasant or unpleasant. One way works just as well as the other. But the fact remains; it was your general expectations that resulted in a specific situation of conditioning.

Alpha: Alpha brainwave patterns are associated with a state of wakeful relaxation. Slower and lower in frequency (between 9-14 hertz), alpha waves are dominant when we’re calm and relaxed, but still alert. Alpha waves are associated with states of meditation (your yoga class probably puts you in an alpha state), and also with our ability to be creative.
Today, EEG machines are used for diagnosing epilepsy and sleep disorders, for determining dosages for anesthesia, and measuring the brain activity of people in comas or suffering from brain trauma. EEG machines also continue to play a role in researching and understanding brainwave entrainment and developing new and better methods for delivering the benefits of this form of brainwave modification. 
The phenomena of brainwave entrainment was first described in the scientific literature in 1973 by Gerald Oster in results published in an article in Scientific American entitled, “Auditory Beats in the Brain”. He showed that a specific brainwave could be induced when a person heard two separate, but closely related, sound frequencies, one in each ear. He discovered that when the frequencies heard by each ear differed by about 10 hertz, the brainwave pattern of the person hearing the sound would synchronize to the difference between the two frequencies. For example, if the person heard a 410 hertz sound in one ear and a 400 hertz sound in the other ear, their brainwaves would stabilize at the difference between the two, or 10 hertz. This technique is called binaural beats, and it is a fundamental principle of brainwave entrainment methods.
Research suggests the negative effects of stress on the body seem to be exaggerated in people who are inactive, a phenomenon called”stress-induced/exercise deficient” phenotype. Because we react to stress by experiencing changes in our neuro-endocrine systems, regular exercise is protective because it regulates various metabolic and psychological processes in the body, including reinforcing our natural circadian rhythms, sleep/wake cycles, moods and blood sugar levels.
The functional role of neural oscillations is still not fully understood;[6] however they have been shown to correlate with emotional responses, motor control, and a number of cognitive functions including information transfer, perception, and memory.[7][8][9] Specifically, neural oscillations, in particular theta activity, are extensively linked to memory function, and coupling between theta and gamma activity is considered to be vital for memory functions, including episodic memory.[10][11][12]